5-78034375-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_003664.5(AP3B1):c.2880C>T(p.Ala960Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00371 in 1,611,118 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003664.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AP3B1 | NM_003664.5 | c.2880C>T | p.Ala960Ala | synonymous_variant | Exon 24 of 27 | ENST00000255194.11 | NP_003655.3 | |
AP3B1 | NM_001271769.2 | c.2733C>T | p.Ala911Ala | synonymous_variant | Exon 24 of 27 | NP_001258698.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00377 AC: 572AN: 151908Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00467 AC: 1172AN: 251116Hom.: 8 AF XY: 0.00456 AC XY: 619AN XY: 135732
GnomAD4 exome AF: 0.00370 AC: 5404AN: 1459092Hom.: 35 Cov.: 30 AF XY: 0.00353 AC XY: 2565AN XY: 725990
GnomAD4 genome AF: 0.00376 AC: 572AN: 152026Hom.: 11 Cov.: 32 AF XY: 0.00451 AC XY: 335AN XY: 74320
ClinVar
Submissions by phenotype
not specified Benign:2
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Ala960Ala in exon 24 of AP3B1: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 0.4% (32/8600) of E uropean American chromosomes from a broad population by the NHLBI Exome Sequenci ng Project (http://evs.gs.washington.edu/EVS; dbSNP rs62001052). -
Hermansky-Pudlak syndrome 2 Benign:2
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not provided Benign:2
AP3B1: BP4, BS2 -
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Hermansky-Pudlak syndrome Uncertain:1
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Autoinflammatory syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at